The timer at the end of level 6 of Special Edition appears to have some behavior differences between the floppy and WHDLoad versions. Appending "NOCACHES" and "NOMMUS" to the tooltypes for the game icon appears to have it match the behavior of the floppy version more. This should really only be done for runners on actual Amigas that have processors with MMU's (so anything that isn't a EC version of a processor, ie. the 68EC020 like in the 1200)

Ok, so I did a bit more digging into this. The MMU makes the chances of getting a instant timer start on level 6 higher than on a system without a MMU. Options are still the same, but wanted to clarify.